The Hidden Story of Heterogeneous B-raf V600E Mutation Quantitative Protein Expression in Metastatic Melanoma—Association with Clinical Outcome and Tumor Phenotypes

Abstract

In comparison to other human cancer types, malignant melanoma exhibits the greatest amount of heterogeneity. After DNA-based detection of the BRAF V600E mutation in melanoma patients, targeted inhibitor treatment is the current recommendation. This approach, however, does not take the abundance of the therapeutic target, i.e., the B-raf V600E protein, into consideration. As shown by immunohistochemistry, the protein expression profiles of metastatic melanomas clearly reveal the existence of inter- and intra-tumor variability. Nevertheless, the technique is only semi-quantitative. To quantitate the mutant protein there is a fundamental need for more precise techniques that are aimed at defining the currently non-existent link between the levels of the target protein and subsequent drug efficacy. Using cutting-edge mass spectrometry combined with DNA and mRNA sequencing, the mutated B-raf protein within metastatic tumors was quantitated for the first time. B-raf V600E protein analysis revealed a subjacent layer of heterogeneity for mutation-positive metastatic melanomas. These were characterized into two distinct groups with different tumor morphologies, protein profiles and patient clinical outcomes. This study provides evidence that a higher level of expression in the mutated protein is associated with a more aggressive tumor progression. Our study design, comprised of surgical isolation of tumors, histopathological characterization, tissue biobanking, and protein analysis, may enable the eventual delineation of patient responders/non-responders and subsequent therapy for malignant melanoma.

Metastasis of Uveal Melanoma with Monosomy-3 Is Associated with a Less Glycogenetic Gene Expression Profile and the Dysregulation of Glycogen Storage

“…Such an additive outcome was indeed reported in a previous gene set enrichment study, which demonstrated the downregulation of genes involved in oxidative phosphorylation in the muscle biopsies of human diabetic patients, with an average reduction of 20% per gene [ 64 ]. Since the mRNA levels may not always be reflecting the amount of active proteins [ 65 ], further studies at the protein level would also be invaluable for determining the functional consequences of this altered gene expression profile on the glycogen metabolism with regard to the monosomy-3 status.…”

A high-stringency blueprint of the human proteome

“…Reviewing the underlying causes of breast cancer also demonstrates that coupling genomic/transcriptomic data with proteomic/phosphoproteomic analysis was more insightful than any individual approach. Of note, melanoma tumour genomic BRAF driver mutations match corresponding protein sequences 97 , illustrating that proteomic landscapes add value to genomic data, when considered with patient tumour histopathology and clinical metadata 98 .…”

Biobanks in oncology: global experience and Russian reality

“…Среди последних исследований в онкологии с привлечением ресурса биобанков следует процитировать передовое исследование по гетерогенности метастатической меланомы в отношении экспрессии гена B-rafV600 и возможности его количественного определения методом масс-спектрометрии в сочетании с секвенированием ДНК и мРНК. Анализ количества белка B-raf позволил выявить отдельные дополнительные группы прогноза ответа на терапию BRAF и MEK-ингибиторами среди пациентов с B-raf-положительной метастатической опухолью [42].…”